Variant report

Variant	rs57325238
Chromosome Location	chr6:163952120-163952121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:163952024-163952224	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163832850..163838270-chr6:163950827..163956360,5	K562	blood:
2	chr6:163951535..163954078-chr6:163954622..163957067,3	K562	blood:

Variant related genes	Relation type
QKI	TF binding region
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11964059	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56098044	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59777232	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73013596	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73017335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021403	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73021406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7739152	1.00[EUR][1000 genomes]
rs7752293	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754132	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7755889	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7756950	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1027863	chr6:163934616-163965216	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
2	chr6:163929800-163957000	Weak transcription	Primary B cells from cord blood	blood
3	chr6:163935200-163952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:163935200-163958800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:163935200-163959400	Weak transcription	Lung	lung
6	chr6:163936800-163953600	Enhancers	Brain Hippocampus Middle	brain
7	chr6:163936800-163957400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:163939800-163956200	Enhancers	Brain Anterior Caudate	brain
9	chr6:163940200-163983000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:163944000-163952200	Weak transcription	Gastric	stomach
11	chr6:163944000-163952200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:163944200-163952200	Weak transcription	K562	blood
13	chr6:163944200-163953600	Weak transcription	GM12878-XiMat	blood
14	chr6:163944200-163957400	Enhancers	Brain Substantia Nigra	brain
15	chr6:163944600-163952400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:163945000-163957400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:163945800-163955800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:163946200-163955800	Enhancers	Liver	Liver
19	chr6:163946600-163952400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:163946800-163952200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:163947200-163953600	Enhancers	Adipose Nuclei	Adipose
22	chr6:163947800-163952200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr6:163947800-163952800	Enhancers	Brain Angular Gyrus	brain
24	chr6:163947800-163953600	Enhancers	HSMMtube	muscle
25	chr6:163948400-163958400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:163948600-163959000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:163948600-163964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:163949000-163952600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:163949000-163952600	Enhancers	Colon Smooth Muscle	Colon
30	chr6:163949000-163952600	Enhancers	NHEK	skin
31	chr6:163949000-163958000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:163949200-163955800	Enhancers	Brain Germinal Matrix	brain
33	chr6:163949400-163952200	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr6:163949400-163952600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr6:163949400-163952800	Enhancers	Osteobl	bone
36	chr6:163949400-163953000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:163949400-163959200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:163949600-163952400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:163949600-163953400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:163949600-163975200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:163949800-163953200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:163950000-163952400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:163950000-163952600	Enhancers	HMEC	breast
46	chr6:163950000-163954400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:163950200-163952200	Enhancers	Rectal Smooth Muscle	rectum
48	chr6:163950200-163952800	Enhancers	Fetal Brain Female	brain
49	chr6:163950200-163954200	Enhancers	Fetal Muscle Leg	muscle
50	chr6:163950400-163952600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links